Changeset 10600


Ignore:
Timestamp:
2019-01-28T21:07:57+01:00 (18 months ago)
Author:
nicolasmartin
Message:

Review inclusion of RELEASE_NOTES in the index and several changes in formatting

Location:
NEMO/trunk
Files:
3 edited

Legend:

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  • NEMO/trunk/RELEASE_NOTES.rst

    r10598 r10600  
    22Release Notes 
    33************* 
    4  
    5 .. contents:: 
    6    :local: 
    74 
    85New sea-ice component SI3 (in place of LIMx) 
     
    107 
    118- Physics 
     9 
    1210  - Lateral melting 
    13   - Melt ponds: constant or :doi:`10.1175/JCLI-D-11-00078.1 <Holland et al. 2012>` formulation (and soon topographic melt ponds) 
    14   - Ice-atm. drags from :doi:`10.1029/2012JD017630 <Lupkes et al. 2012>` (depending on ice concentration) or :doi:`10.1002/2014JD022418 <Lupkes et al. 2015>` (depending on sea ice concentration and atm. stability) 
    15   - Landfast ice (:doi:`10.1002/2016JC012006 <Lemieux et al. 2016>`) 
     11  - Melt ponds: constant or :doi:`Holland et al. 2012<10.1175/JCLI-D-11-00078.1>` formulation (and soon topographic melt ponds) 
     12  - Ice-atm. drags from :doi:`Lupkes et al. 2012<10.1029/2012JD017630>` (depending on ice concentration) or :doi:`Lupkes et al. 2015<10.1002/2014JD022418>` (depending on sea ice concentration and atm. stability) 
     13  - Landfast ice (:doi:`Lemieux et al. 2016<10.1002/2016JC012006>`) 
    1614 
    1715- Numerics 
     16 
    1817  - Advection: Ultimate-Macho scheme 
    19   - Rheology: adaptive EVP (:doi:`10.1016/j.ocemod.2016.03.004 <Kimmritz et al. 2017>`) 
     18  - Rheology: adaptive EVP (:doi:`Kimmritz et al. 2017<10.1016/j.ocemod.2016.03.004>`) 
    2019  - Coupling interface: conductivity as surface forcing instead of heat fluxes (Met Office requirement) 
    21      
     20 
    2221- Performance: all thermodynamics in 1D and reduced mpp communications 
    23      
    2422- Usability (users & developers friendly) 
    25   - Comprehensive set of outputs (universal units and understandable names + includes cmip) 
     23 
     24  - Comprehensive set of outputs (universal units and understandable names + includes CMIP) 
    2625  - New architecture and namelist 
    2726  - All processes can be decoupled from each other (switch on/off) 
     
    4443 
    4544- Fix for tracer conservation with split explicit free surface 
    46 - Bulk formulae : move to aerobulk package (:doi:`10.1175/JPO-D-16-0169.1 <Brodeau et al. 2016>`), i.e. NCAR, COARE and ECMWF bulk 
    47                   (remove Clio and MFS bulk) 
     45- Bulk formulae : move to aerobulk package (:doi:`Brodeau et al. 2016<10.1175/JPO-D-16-0169.1>`), i.e. NCAR, COARE and ECMWF bulk (remove Clio and MFS bulk) 
    4846- Wetting and drying 
    4947- Added tidal self attraction and loading either read from a file or from usual "scalar" approximation 
     
    5250- iso-neutral mixing (iso and triad operators): 
    5351  add the Method of Stabilizing Correction (MSC) (more accurate calculation) + add a bilaplacian case 
    54 - Lateral physics (LDF): scale aware setting of eddy viscosity and diffusivity 
    55 - Vorticity: 2 new energy conserving scheme: 
    56   ENT with Coriolis defined at T-point (better for Flux form) and 
    57   EET a variant of EEN where e3t is used instead of e3f 
    58   (solved the issue with e3f specification but is not enstrophy conserving)  
     52- Lateral physics (``LDF``): scale aware setting of eddy viscosity and diffusivity 
     53- Vorticity: 2 new energy conserving scheme: ENT with Coriolis defined at T-point (better for Flux form) and EET a variant of EEN where e3t is used instead of e3f (solved the issue with e3f specification but is not enstrophy conserving)  
    5954 
    6055Test Cases 
     
    6257 
    6358The first test cases available for now are: 
     59 
    6460- ``CANAL``: east-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex) 
    65 - ``ICE_AGRIF``: east-west + north-south periodic channel. The common configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the key_agrif in the cpp keys. 
    66 - ``ISOMIP``: simple box configuration with an ice shelf with simple geometry on top. The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. The exact original setup is described ​here. 
    67 - ``LOCK-EXCHANGE``:classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. It has been used by several authors including Burchard and Bolding (2002) and Ilıcak et al. (2012). The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing 
    68 - ``OVERFLOW``: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by Ilıcak et al. (2012) 
    69 - ``VORTEX``: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. It is implemented here with an online refined subdomain (thanks to AGRIF library) out of which the vortex propagates. It serves as a benchmark to diagnose nesting errors as in Debreu et al. (2012), Penven et al. (2006) and Spall and Holland (1991) 
    70 - ``WAD``: a set of simple closed basin geometries for testing the Wetting and drying capabilities. Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge.  
     61- ``ICE_AGRIF``: east-west + north-south periodic channel. The common configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the ``key_agrif`` in the cpp keys 
     62- ``ISOMIP``: simple box configuration with an ice shelf with simple geometry on top. The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. The exact original setup is described ​here 
     63- ``LOCK-EXCHANGE``: classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. It has been used by several authors including Burchard and Bolding (2002) and :doi:`Ilıcak et al. (2012)<10.1016/j.ocemod.2011.10.003>`. The ``LOCK EXCHANGE`` experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing 
     64- ``OVERFLOW``: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by :doi:`Ilıcak et al. (2012)<10.1016/j.ocemod.2011.10.003>` 
     65- ``VORTEX``: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. It is implemented here with an online refined subdomain (thanks to ``AGRIF`` library) out of which the vortex propagates. It serves as a benchmark to diagnose nesting errors as in :doi:`Debreu et al. (2012)<10.1016/j.ocemod.2012.03.003>`, :doi:`Penven et al. (2006)<10.1016/j.ocemod.2005.05.002>` and :doi:`Spall and Holland (1991)<10.1175/1520-0485(1991)021<0205:ANPEMF>2.0.CO;2>` 
     66- ``WAD``: a set of simple closed basin geometries for testing the wetting and drying capabilities. Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge 
    7167 
    7268New Reference configurations 
     
    7470 
    7571``AGRIF_DEMO``: 2 interlocked zooms (1:4 & 1:3) in the Nordic Seas + 1 zoom (1:1) at the equator 
     72 
    7673``SPITZ12``: regional configuration around the Svalbard archipelago  
    7774 
     
    8077 
    8178Coupled interface to external wave model 
     79 
    8280Large scale wave interaction process added in momentum and tracer equations  
    8381 
     
    8583======================================================= 
    8684 
    87 - The passive tracers transport component was redesigned toward a modular structure and users can enable each module directly through logical flags in namelist_top (no more fortran macros!). 
    88 - :doc:`tracers <TOP on-line user documentation>` 
    89 - ``TOP`` currently accounts for the following 5 modules: 
    90   ``CFC`` contains inorganic carbon tracers (CFC11/CFC12/SF6), 
    91   ``MY_TRC`` is a template for new modules (or external couplings), 
    92   ``AGE`` deals with water age tracking, 
    93   ``C14`` as a radiocarbon passive tracer, and 
    94   the companion ecosystem model ``PISCES``. 
    95 - A generalized infrastructure was developed to handle the prescription of either surface, coastal, or open boundaries conditions for each passive tracer. 
    96 - A new configuration, named ORCA2_OFF_TRC, was created to provide a benchmark simulation environment to deal with inert carbon tracers dynamics by exploiting the offline coupling with NEMO. 
     85- The passive tracers transport component was redesigned toward a modular structure and users can enable each module directly through logical flags in namelist_top (no more fortran macros!) 
     86- :doc:`TOP on-line user documentation<tracers>` 
     87- TOP currently accounts for the following 5 modules: ``CFC`` contains inorganic carbon tracers (CFC11/CFC12/SF6), ``MY_TRC`` is a template for new modules (or external couplings), ``AGE`` deals with water age tracking, ``C14`` as a radiocarbon passive tracer, and the companion ecosystem model ``PISCES`` 
     88- A generalized infrastructure was developed to handle the prescription of either surface, coastal, or open boundaries conditions for each passive tracer 
     89- A new configuration, named ``ORCA2_OFF_TRC``, was created to provide a benchmark simulation environment to deal with inert carbon tracers dynamics by exploiting the offline coupling with NEMO 
    9790- PISCES model contains new developments and modifications: 
    98   - Particulate Organic Carbon (POC) component comes with a new liability scheme, while the former Kriest parametrisation was superseded; 
     91 
     92  - Particulate Organic Carbon (POC) component comes with a new liability scheme, while the former Kriest parametrisation was superseded 
    9993  - A complex iron chemistry scheme is now available, with an improved description of ligands for the marine iron cycle 
    100   - Carbonate chemistry is based on MOCSY 2.0 routines (see :doi:`10.5194/gmd-8-485-2015 <Orr and Epitalon, 2015>`), by complying also with CMIP6 standards. 
     94  - Carbonate chemistry is based on MOCSY 2.0 routines (see :doi:`10.5194/gmd-8-485-2015 <Orr and Epitalon, 2015>`), by complying also with CMIP6 standards 
    10195  - Ecosystem components can be optionally modelled by means of explicit nutrient quotas (PISCES-QUOTA)  
    10296 
     
    106100- Reduce number of MPI communications 
    107101  (suppression of redundant communications, gather multiple communications into one) 
    108 - Use of MPI-3 asynchronous routines for performance (use key_mpi2 if MPI-3 not available) 
     102- Use of MPI-3 asynchronous routines for performance (use ``key_mpi2`` if MPI-3 not available) 
    109103- Back to standard dynamical allocation (remove of wrk_alloc/dealloc statements) 
    110 - :xios:`<XIOS software>` for IOs version 2.5 as default, and optionally available for restarts  
     104- :xios:`XIOS software<>` for IOs version 2.5 as default, and optionally available for restarts  
    111105 
    112106Simplification and robustness 
    113107============================= 
    114108 
    115 - Revised structure of namelist_ref/_cfg and default reference values. 
    116 - Lateral physics (LDF): simplification of user interface and removal of CPP keys 
    117 - Vertical physics (ZDF) (modularity, share shear production calculation between TKE and GKS, removal of all ZDF CPP keys, removal of avmu & avmv, minimization of MPP comm.: ~15 removed) 
    118   Remove the split-explicit ZDF scheme for both TRA and DYN 
    119   Remove the acceleration of convergence 
    120   Generalised lbc_lnk and lbc_nfd 
    121   Unify mppini 
    122   Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns 
    123   MPI Message passing re coded 
    124   Configuration interface completely rewritten 
    125   (DOM module mainly suppressed , and in place: domain_cfg.nc file, or usr_def module)  
     109- Revised structure of ``namelist_ref`` / ``namelist_cfg`` and default reference values 
     110- Lateral physics (``LDF``): simplification of user interface and removal of CPP keys 
     111- Vertical physics (``ZDF``) (modularity, share shear production calculation between TKE and GKS, removal of all ZDF CPP keys, removal of ``avmu`` & ``avmv``, minimization of MPP comm.: ~15 removed) 
     112- Remove the split-explicit ZDF scheme for both ``TRA`` and ``DYN`` 
     113- Remove the acceleration of convergence 
     114- Generalised ``lbc_lnk`` and ``lbc_nfd`` 
     115- Unify mppini 
     116- Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns 
     117- MPI Message passing re coded 
     118- Configuration interface completely rewritten (``DOM`` module mainly suppressed , and in place: ``domain_cfg.nc`` file, or ``usr_def`` module)  
    126119 
    127120Collaborative Development Environment 
    128121===================================== 
    129122 
    130 - Access to information on NEMO wiki reorganised through portals for users/developers/System Team and complete refactoring of all wiki pages and their layout 
    131 - Reorganisation of SVN repository to be compliant with usual directory tree and facilitate building of NEMO executable 
    132 - Define and install a separate repository for test cases to all easy contributions from the NEMO Users Community 
    133 - :forge:`discussion <Forums>` created 
    134 - ​:nemo:`<NEMO public web site>` has been cleaned and is now much nicer (using Wordpress instead of EzP) 
     123- Access to information on wiki reorganised through portals for users/developers/System Team and complete refactoring of all pages and their layout 
     124- Reorganisation of SVN repository to be compliant with usual directory tree and facilitate building of the executable 
     125- Define and install a separate repository for test cases to all easy contributions from the community 
     126- :forge:`Forums<discussion>` created 
     127- :website:`Public web site<>` has been revamped and cleaned using Wordpress 
    135128- New mailing lists have been set up 
    136129- Improvements of reliability through automatic and regular testing of the changes made in repository  
  • NEMO/trunk/doc/rst/source/NEMO_guide.rst

    r10598 r10600  
    1616 
    1717.. toctree:: 
    18    :hidden: 
    19    :caption: What's new in NEMO 4.0 
     18   :hidden: 
    2019 
    21    release_notes 
     20   release_notes 
    2221 
    2322.. toctree:: 
    24    :hidden: 
    25    :caption: Getting started 
     23   :hidden: 
     24   :caption: Getting started 
    2625 
    27    install 
    28    configurations 
    29    test_cases 
     26   install 
     27   configurations 
     28   test_cases 
    3029 
    3130.. toctree:: 
    32    :hidden: 
    33    :caption: Setup your configuration 
     31   :hidden: 
     32   :caption: Setup your configuration 
    3433 
    35    setup 
    36    diagnostics 
    37    tools 
     34   setup 
     35   diagnostics 
     36   tools 
    3837 
    3938.. toctree:: 
    40    :hidden: 
    41    :caption: Advanced use 
     39   :hidden: 
     40   :caption: Advanced use 
    4241 
    43    zooms 
    44    coupling 
    45    data_assimilation 
    46    tracers 
     42   zooms 
     43   coupling 
     44   data_assimilation 
     45   tracers 
    4746 
    4847.. toctree:: 
    49         :hidden: 
    50         :caption: Contributions are welcome! 
     48   :hidden: 
     49   :caption: Contributions are welcome! 
    5150 
    52         contributing 
     51   contributing 
    5352 
    5453.. toctree:: 
    55    :hidden: 
    56    :caption: Glossary 
     54   :hidden: 
     55   :caption: Glossary 
    5756 
    58    definitions 
     57   definitions 
    5958 
    6059.. include:: readme.rst 
     
    6564====================== 
    6665 
    67 .. bibliography:: references.bib 
    68    :all: 
    69    :style: unsrt 
    70    :labelprefix: R 
     66.. bibliography:: references.bib 
     67   :all: 
     68   :style: unsrt 
     69   :labelprefix: R 
    7170 
    7271Disclaimer 
  • NEMO/trunk/doc/rst/source/conf.py

    r10599 r10600  
    1515version = '4.0' 
    1616# The full version, including alpha/beta/rc tags 
    17 release = '4.0' 
     17release = 'release-4.0' 
    1818 
    1919 
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